Difference between revisions of "Team:Newcastle/Software"

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                 <h3>OpenTrons</h3>
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                 <h3>Alternative Roots</h3>
  
 
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                 <h1 class="display-1">Overview</h1>
 
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                     <p style="font-size:100%">As part of our lab work a number of the team members have become familiar with the Opentrons. Which required learning python, the coding language used by the robot. This machine has been very useful in the lab as we have been able to automate the pipetting increasing the accuracy of our experiments and saving time in the labs.</p>
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                     <p style="font-size:100%">A significant proportion of the Alternative Roots project was based on software, whether that was for automation of experiments via the Opentrons OT-2 or small-scale plant growth via our NH-1. Both systems were carefully programmed by our team for efficiency and reliability.</p>
  
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                     <p style="font-size:100%">We have 3D printed custom labware which can hold a variety of beakers and tubes through a removable acrylic lid cut to specification. This equipment also doubles up as a cold deck when filled with ice, allowing us to heat shock transform <i>E.coli</i>. There has also been a number of kill curves performed on pseudomonas to identify a suitable anti-biotic which can then be used as our test to identify if our transformations have worked. Gentamycin and Streptomycin being two that were a success.</p>
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                     <p style="font-size:100%">Newcastle were fortunate to win an Opentrons OT-2 liquid-handling robot in 2018. The OT-2 is programmed in Python and is equipped with two pipettes capable of pipetting between 1 and 300 µL as well as a temperature module, capable of maintaining temperatures between 0-100 °C. We have created and deposited code that allows OT-2 users to automate small-scale (100 µL) heat-shock transformations of <i>E. coli</i>. The value of this code was demonstrated when it was used to perform a statistical ‘Definitive Screening Design’ screen to examine the impact that transformation buffers have on transformation efficiency. As a result, we identified a new buffer composition with 10-fold improved transformation efficiency. Perhaps more importantly, the combination of the code and the robot resulted in greater reliability than the manual protocol.</p>
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                    <p style="font-size:100%">The Python script and the protocol can be found here. The code has been done in a way where it can be easily adapted for alternate uses. The code and results can be found here!!!</p>
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                <h1 class="display-2">References & Attributions</h1>
 
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            <h3 class="subhead">Transformation Protocol</h3>
 
 
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                <p style="font-size:100%">Using the OT-2 and the Peltier thermocycler (TempDeck), a robust a <a href="https://github.com/jbird1223/Newcastle-iGEM/blob/master/OT-2%20Protocol/Transformation.py" class="black">Transformation Buffer</a>(TB) was developed that could be used to rapidly transform Escherichia coli DH5a in a microtitre plate format. This was developed as part of a Biodesign Automation (BDA) workflow that would allow us to optimise TB using a Design of Experiments (DoE) methodology. Our initial automated transformation workflow produced E. <i>coli</i> with a transformation efficiency (TrE) of 1.89 x 10<sup>4</sup> and scoping experiments determined that the 96 well plate format decreases TrE by a factor of 100 (Figure ...) </p>
 
  
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                <p style="font-size:100%">With optimisation of the TB, automated TrE was increased to 2.21 x 10<sup>6</sup>, a 100x increase on the initial workflow (Figure ...). More importantly, it appeared to be highly robust, with every aliquot producing some successful transformants and it was rapid, without need for excessive centrifugation and incubation.</p>
 
  
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<p class="about-para"><font size="2"><strong>Attributions: Umar Farooq
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                    <p style="text-align:center"><br>Figure 1.0; Falcon tube rack.</p>
 
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                    <p style="text-align:center"><br>Figure 1.1; 3D printed rack/ice holder.</p>
 
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Latest revision as of 23:24, 17 October 2018

Alternative Roots/Software

Alternative Roots

Software Overview

OpenTrons NH-1

Overview

A significant proportion of the Alternative Roots project was based on software, whether that was for automation of experiments via the Opentrons OT-2 or small-scale plant growth via our NH-1. Both systems were carefully programmed by our team for efficiency and reliability.

Newcastle were fortunate to win an Opentrons OT-2 liquid-handling robot in 2018. The OT-2 is programmed in Python and is equipped with two pipettes capable of pipetting between 1 and 300 µL as well as a temperature module, capable of maintaining temperatures between 0-100 °C. We have created and deposited code that allows OT-2 users to automate small-scale (100 µL) heat-shock transformations of E. coli. The value of this code was demonstrated when it was used to perform a statistical ‘Definitive Screening Design’ screen to examine the impact that transformation buffers have on transformation efficiency. As a result, we identified a new buffer composition with 10-fold improved transformation efficiency. Perhaps more importantly, the combination of the code and the robot resulted in greater reliability than the manual protocol.







References & Attributions

Attributions: Umar Farooq